I am happy to announce the launch of a new Arabidopsis genomics resource! Check out arabidopsislyrata.org Now you can easily look at the natural genetic variation across the entire species range of A. lyrata and A. arenosa.

Come join our lab in Sussex, UK for a PhD on TEs, on centromeres, on the genome ecosystem! Exciting times for TE:genome dynamics given the rate of T2T sequencing. Please circulate! www.findaphd.com/phds/project...

Evolutionary dynamics of transposable elements in the genome ecosystem of eukaryotes at University of Sussex on FindAPhD.com

PhD Project - Evolutionary dynamics of transposable elements in the genome ecosystem of eukaryotes at University of Sussex, listed on FindAPhD.com

findaphd.com

📢 Three new #bioRxiv preprints from our team on holocentric chromosomes. Together, they connect centromere repeat evolution, karyotype dynamics, and meiotic recombination outcomes, revealing how holocentric genomes evolve and function. 🧬👇

FastGA -> ALNview; step into the centromeric matrix! github.com/thegenemyers Probably the best dot plot software on the planet...

Wonderful (and humble) essay on mentorship by Brandon Gaut, on occasion of Brandon receiving the inaugural Mentorship Award of @genetics-gsa.bsky.social. I hope this will be widely read! academic.oup.com/genetics/art...

Happy to share our new work with exciting findings, incl. different centromere organisations and all kinds of weird polyploids giving rise to the mysterious carnivorous sundews! Great word led by my postdoc Laura in collaboration with @plantgenomes.bsky.social www.biorxiv.org/content/10.1...

Contrasting centromere structures in carnivorous sundews uncover a dynamic evolutionary trajectory shaped by polyploidy and chromosomal remodeling

Sundews (Drosera) are carnivorous plants that capture prey using mucilage-producing glands with both secretory and absorptive functions. Within a remarkably diverse clade that includes the Venus flytr...

biorxiv.org

Our new preprint on somatic TE transposition in A. thaliana is out! It looks like TEs jump like crazy! Led by the amazing @heenaa02.bsky.social and with Hans-Wilhelm Nuetzmann from Exeter www.biorxiv.org/content/10.1...

Somatic mobility of transposons is explosive and shaped by distinct integration biases in Arabidopsis thaliana

Background The movement of transposable elements (TEs) in somatic cells generates genetic and phenotypic diversity across the soma of individual organisms. This process is especially important in plan...

biorxiv.org

6/ 🙏 Huge thanks to the amazing collaborators and co-authors who made this work possible! 🧑‍🔬 Basile Leduque, Leandro Quadrana, Keith Slotkin, Alexandros Bousios (@abousios.bsky.social) & Hans-wilhelm Nuetzmann

5/ 💻 Surprise package! We developed a custom pipeline, deNOVOEnrich, to profile somatic TE insertions from TEd-seq short-read data. Using split-read mapping, we pinpoint new somatic insertions at base-pair resolution 🧬🔍 Check it out: github.com/hAmbreen02/d...

GitHub - hAmbreen02/deNOVOEnrich: Identification of de novo transposon insertion sites from targeted sequencing data

Identification of de novo transposon insertion sites from targeted sequencing data - hAmbreen02/deNOVOEnrich

github.com

4/ 🔥 Somatic insertion hotspots of the EVADE transposon are enriched at environmentally responsive genes 🌄 - including Resistance gene and biosynthetic gene clusters. Is stress guiding TE activity, or are TEs tuning stress responses? Somatic genome plasticity 🧬

3/ 🧬 Our work shows somatic TE activity in Arabidopsis is non‑random and family‑specific. Different TE families prefer distinct genomic niches - is it driven by underlying epigenetic code, or are they avoiding conflict in a shared genome ecosystem? 🤔

2/ Combining distinct experimental conditions, we traced a roadmap of expected TE movement in somatic cells 🌿, capturing ~200K new TE insertions across multiple families in the process.

1/📢News from TE diary - Somatic transposition in Arabidopsis is more explosive than we imagined! Thrilled to share our latest findings - TEs make new somatic insertions en masse, reshaping the somatic genome🧬with surprising frequency🍃 @abousios Hans-Wilhelm Nuetzmann www.biorxiv.org/content/10.1...

Somatic mobility of transposons is explosive and shaped by distinct integration biases in Arabidopsis thaliana

Background The movement of transposable elements (TEs) in somatic cells generates genetic and phenotypic diversity across the soma of individual organisms. This process is especially important in plan...

biorxiv.org

1/2 Somatic TE transposition in plants is getting traction again (70 years after McClintock's discovery of "controlling elements")! A very large collection of somatic TE insertions in A. thaliana described by Ambreen et al.(www.biorxiv.org/content/10.1...).

2/2 See also @movillome.bsky.social's paper from my lab on using PacBio long-read sequencing to discover somatic TE insertions with high sensitivity and specificity in an unbiased manner -- an excellent complement to powerful short-read based enrichment methods (www.biorxiv.org/content/10.1...)

1/7 I am very excited to announce our🌹NEW PAPER OUT IN 𝑁𝐴𝑇𝑈𝑅𝐸!🌹 𝐃𝐑𝐈𝐕𝐄 𝐓𝐎 𝐒𝐔𝐑𝐕𝐈𝐕𝐄: Bimodal centromeres in pentaploid dogroses shed light on their unique meiosis With the Ritz and Kovařík labs we show a potential role for centromeres on 𝘙𝘰𝘴𝘢 𝘤𝘢𝘯𝘪𝘯𝘢 bizarre reproduction! www.nature.com/articles/s41...

Bimodal centromeres in pentaploid dogroses shed light on their unique meiosis - Nature

Insights into the dogrose genome and centromeres explain their ability to achieve stable sexual reproduction.

nature.com

Nature research paper: Bimodal centromeres in pentaploid dogroses shed light on their unique meiosis https://go.nature.com/407PRGm

Bimodal centromeres in pentaploid dogroses shed light on their unique meiosis - Nature

Insights into the dogrose genome and centromeres explain their ability to achieve stable sexual reproduction.

go.nature.com

NIH funding supporting the HMMER and Infernal software projects has been terminated. NIH states that our work, as well as all other federally funded research at Harvard, is of no benefit to the US.

💥🥳 At long last, our latest paper is out! Gag proteins of endogenous retroviruses are required for zebrafish development www.pnas.org/doi/10.1073/... Led heroically by Sylvia Chang & @jonowells.bsky.social A study which has changed the way I think of #transposons! No less! 🧵 1/n

Gag proteins encoded by endogenous retroviruses are required for zebrafish development | PNAS

Transposable elements (TEs) make up the bulk of eukaryotic genomes and examples abound of TE-derived sequences repurposed for organismal function. ...

pnas.org

📢 Excited to share our work out now in @nature.com! 📢 We present the phased pan-genome of tetraploid European potato, based on 10 historical cultivars representing 85% of European potato diversity. Learn more below! 🔗 www.nature.com/articles/s41... 1/7

The phased pan-genome of tetraploid European potato - Nature

A haplotype-resolved pan-genome of autotetraploid European potato founder lines shows high nucleotide diversity at remarkably low haplotype diversity, which is probably the result of hybridization eve...

nature.com

Excited to share our preprint on the molecular architecture of heterochromatin in human cells 🧬🔬w/ @jpkreysing.bsky.social, @johannesbetz.bsky.social, @marinalusic.bsky.social, Turoňová lab, @hummerlab.bsky.social @becklab.bsky.social @mpibp.bsky.social 🔗 Preprint here tinyurl.com/3a74uanv

1/ Transposable elements are often called "jumping genes" because they mobilize within genomes. 🧬 But did you know they can also jump 𝘣𝘦𝘵𝘸𝘦𝘦𝘯 cells? 🤯 Our new study reveals how retrotransposons invade the germline directly from somatic cells. www.biorxiv.org/content/10.1... A short thread 🧵👇

This Editorial by Brandon S. Gaut and Claudia A. M. Russo provides some nice insight into how #SocietyJournals work, and why it pays for Scientists to publish with #SocietyOwned Journals. 👇 A Message From the Editors-in-Chief academic.oup.com/mbe/article/... #PlantScience #SciencePublishing

A Message From the Editors-in-Chief

We have been Co-Editor-in-Chiefs of Molecular Biology and Evolution (MBE) for 2 years now. In that time, we have learned a great deal about the science of

academic.oup.com

🚨New paper published in @nature.com! Using pan-genetics across the Solanum genus🍅🥔🍆we reveal why gene duplications🧬are major contingencies in crop engineering. My postdoc work in the Lippman lab @CSHL, collab. with @katiejenike.bsky.social @mikeschatz.bsky.social chatz.bsky.social and many others!

Solanum pan-genetics reveals paralogues as contingencies in crop engineering - Nature

Gene duplication and subsequent paralogue diversification are major obstacles to genotype-to-phenotype predictability.

nature.com

Join us for the first seminar in a new series by @IntlGeneticsFed! "Biodiversity Genomics – African & European Perspectives" 📅 March 4, 2025 at 12:00 GMT 🔗 Register now: forms.office.com/r/e1MgVyfCvs

Another piece to add in the emerging golden era of centromere research. Our review of centrophilic transposons in plants @annualreviews.bsky.social with @hendersi.bsky.social and Tetsuji Kakutani. www.annualreviews.org/content/jour...

Centrophilic Retrotransposons of Plant Genomes www.annualreviews.org/content/jour... new review @annualreviews.bsky.social from @abousios.bsky.social, Tetsuji Kakutani, and myself on my favourite type of mobile genetic element

PRESS RELEASE - Professor Uauy appointed as Director of the John Innes Centre Following an international search, we are delighted to announce that Professor @cristobaluauy.bsky.social has been appointed as the next Director of the John Innes Centre. www.jic.ac.uk/press-releas... @ukri.org

Professor Uauy appointed as Director of the John Innes Centre | John Innes Centre

Following an international search, Professor Cristóbal Uauy has been appointed as the next Director of the John Innes Centre. Professor Uauy is internationally recognised for his significant…

jic.ac.uk

We present Rfam-based RNA structural alignments and other structure-based inputs for RNA 3D structure prediction by deep learning. www.biorxiv.org/content/10.1...

Happy to share our recent work about 🥔 pangenome. With HiFi and HiC together, we explore the 31 accessions genome of clonal propagation crops. Not surprisingly, large haplotype diversity hidden on the genome. Lots of breakpoints are TEs. www.nature.com/articles/s41... 1/7

Leveraging a phased pangenome for haplotype design of hybrid potato - Nature

A phased pangenome of potato constructed from 60 wild and cultivated haplotypes shows that substantial hybridization occurred during domestication and enables identification of many putative dele...

nature.com